Relationship between methylation level and gene expression in different genic regions. (a) Promoter; (b) Gene body; (c) TTR. Methylation level was measured using the absolute methylation level but similar results were also obtained using the relative methylation level. Genes are categorized into unmethylated (black line) and methylated ones, the latter of which were further divided into five groups based on the absolute methylation level (from Group 1 of the 20% of genes with the lowest methylation level to Group 5 of the 20% with the highest methylation level). For clarity, we only display 1st, 3rd and 5th groups. Methylation-expression Spearman correlation coefficients along genes and their 2 kb-flanking regions in rice (d) and Arabidopsis (e). The methylation-expression Spearman correlation coefficients were also calculated in TTR and promoter regions using genes without TTR methylation (left to the dashed line) and genes without promoter methylation (right to the dashed line) respectively. Methylation was measured using absolute methylation level (f) or relative methylation level (g). The correlation coefficients were calculated using an overlapping sliding window of 5% of sequence length at a step of 2.5% of sequence length.